view test-data/out.test.log.txt @ 0:eab37e8fea75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
author iuc
date Wed, 14 Feb 2018 06:42:36 -0500
parents
children 9cd937788131
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INFO  @ Mon, 12 Feb 2018 03:40:01: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck test -k /tmp/tmp0xS0Jl/files/000/dataset_21.dat -t HL60.final,KBM7.final -c HL60.initial,KBM7.initial -n output --normcounts-to-file --pdf-report --norm-method median --gene-test-fdr-threshold 0.25 --adjust-method fdr --sort-criteria neg --remove-zero none --gene-lfc-method median 
INFO  @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test 
INFO  @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat  
INFO  @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. 
INFO  @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. 
INFO  @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.RTemplate. 
INFO  @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. 
INFO  @ Mon, 12 Feb 2018 03:40:01: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.Rnw. 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 
INFO  @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final 
INFO  @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 
INFO  @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial 
INFO  @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 
INFO  @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 
INFO  @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt 
DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339	3.4299551007579927 
INFO  @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment 
INFO  @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling 
INFO  @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ... 
DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 
DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 
INFO  @ Mon, 12 Feb 2018 03:40:01: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na  
INFO  @ Mon, 12 Feb 2018 03:40:02: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Welcome to RRA v 0.5.7. 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Skipping gene NA for permutation ... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Skipping gene na for permutation ... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Reading input file... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Computing lo-values for each group... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Computing false discovery rate... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Permuting genes with 9 sgRNAs... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Permuting genes with 10 sgRNAs... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Number of genes under FDR adjustment: 100 
INFO  @ Mon, 12 Feb 2018 03:40:02:   Saving to output file... 
INFO  @ Mon, 12 Feb 2018 03:40:02:   RRA completed. 
INFO  @ Mon, 12 Feb 2018 03:40:02:    
INFO  @ Mon, 12 Feb 2018 03:40:02: End command message. 
INFO  @ Mon, 12 Feb 2018 03:40:02: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na  
INFO  @ Mon, 12 Feb 2018 03:40:03: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Welcome to RRA v 0.5.7. 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Skipping gene NA for permutation ... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Skipping gene na for permutation ... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Reading input file... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Computing lo-values for each group... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Computing false discovery rate... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Permuting genes with 9 sgRNAs... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Permuting genes with 10 sgRNAs... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Number of genes under FDR adjustment: 100 
INFO  @ Mon, 12 Feb 2018 03:40:03:   Saving to output file... 
INFO  @ Mon, 12 Feb 2018 03:40:03:   RRA completed. 
INFO  @ Mon, 12 Feb 2018 03:40:03:    
INFO  @ Mon, 12 Feb 2018 03:40:03: End command message. 
DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... 
INFO  @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 
DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 
INFO  @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP 
DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 
INFO  @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt 
INFO  @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt 
INFO  @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt 
INFO  @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt 
INFO  @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R 
INFO  @ Mon, 12 Feb 2018 03:40:04: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:04:   null device  
INFO  @ Mon, 12 Feb 2018 03:40:04:             1  
INFO  @ Mon, 12 Feb 2018 03:40:04:   Writing to file output_summary.tex 
INFO  @ Mon, 12 Feb 2018 03:40:04:   Processing code chunks with options ... 
INFO  @ Mon, 12 Feb 2018 03:40:04:    1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    2 : keep.source term tex (label = tab1, output_summary.Rnw:37) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    3 : keep.source term verbatim (output_summary.Rnw:77) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    4 : keep.source term verbatim pdf  (output_summary.Rnw:83) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    5 : keep.source term verbatim pdf  (output_summary.Rnw:201) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    6 : keep.source term verbatim pdf  (output_summary.Rnw:345) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    7 : keep.source term verbatim pdf  (output_summary.Rnw:489) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    8 : keep.source term verbatim (output_summary.Rnw:567) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    9 : keep.source term verbatim pdf  (output_summary.Rnw:573) 
INFO  @ Mon, 12 Feb 2018 03:40:04:   10 : keep.source term verbatim pdf  (output_summary.Rnw:691) 
INFO  @ Mon, 12 Feb 2018 03:40:04:   11 : keep.source term verbatim pdf  (output_summary.Rnw:835) 
INFO  @ Mon, 12 Feb 2018 03:40:04:   12 : keep.source term verbatim pdf  (output_summary.Rnw:979) 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04:   You can now run (pdf)latex on ‘output_summary.tex’ 
INFO  @ Mon, 12 Feb 2018 03:40:04:   Error in texi2dvi("output_summary.tex", pdf = TRUE) :  
INFO  @ Mon, 12 Feb 2018 03:40:04:     pdflatex is not available 
INFO  @ Mon, 12 Feb 2018 03:40:04:   Execution halted 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04: End command message. 
INFO  @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf 
INFO  @ Mon, 12 Feb 2018 03:40:04: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04: End command message. 
INFO  @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux 
INFO  @ Mon, 12 Feb 2018 03:40:04: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04: End command message. 
INFO  @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex 
INFO  @ Mon, 12 Feb 2018 03:40:04: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04: End command message. 
INFO  @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc 
INFO  @ Mon, 12 Feb 2018 03:40:04: Command message: 
INFO  @ Mon, 12 Feb 2018 03:40:04:    
INFO  @ Mon, 12 Feb 2018 03:40:04: End command message.